RetrogeneDB ID: retro_meug_2004

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold78703:5181..5547(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS18B
• Ensembl ID: ENSMEUG00000012457
• Aliases: None
• Description: mitochondrial ribosomal protein S18B [Source:HGNC Symbol;Acc:14516]

Sequence

>retro_meug_2004
ATTCCTCTCTCCCTCTATCAGGATGCTCCCTGGAAATATCTGGGTATAGAAAAATTCCTGGCTAGATATGGCTCCTCTCA
GTCTGACTTGACTATAGTTGAAATCACAAAGGTGGCATCCCACTACAGTGAATCTGTAAGACATGCCAATTGAGGGAACA
AAGGTACTGGGAATCTTTACCCTATCTTCCAGGATCAGAAACTCCATGTGGACTTTAGCAAGGAGAAGGACTTCGAGCAA
TTAGTTTGTGCTCACATAGACGTCATCTTCCATGCCCCACACACAGGTGTCTGTATGAAGTAGCATAAGAAGTAGACAAA
GGCTATCCTGAAGGCCAGAGACTATAGGTTTTGCAGTTGCCACATT

Alignment

ORF - retro_meug_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.32 %
• Parental protein coverage: 51.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPVSLYQDAPWEYLETEEYLARYGSRP-VWADYRRNHKGGIPPQRTRKTCIR-GNKVAGNPCPICRDQKL
          IP.SLYQDAPW.YL..E..LARYGS...V..DY..NHKGGIP.Q...KTC...GNK..GN..PI..DQKL
Retrocopy IPLSLYQDAPWKYLGIEKFLARYGSSQ<V*LDYS*NHKGGIPLQ*ICKTCQL>GNKGTGNLYPIFQDQKL

Parental  HVDFRNVKLLEQFVCAHTGVIFHAPYTGVCMKQHKKLTAAILKARDHGLLSYHI
          HVDF...K..EQ.VCAH..VIFHAP.TGVCMK.HKK.T.AILKARD....S.HI
Retrocopy HVDFSKEKDFEQLVCAHIDVIFHAPHTGVCMK*HKK*TKAILKARDYRFCSCHI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_2004 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_2004 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005581	1 retrocopy	retro_chof_505,
Macropus eugenii	ENSMEUG00000012457	10 retrocopies	retro_meug_1183, retro_meug_2004 , retro_meug_2124, retro_meug_215, retro_meug_610, retro_meug_648, retro_meug_696, retro_meug_712, retro_meug_717, retro_meug_734,
Macaca mulatta	ENSMMUG00000006525	1 retrocopy	retro_mmul_900,
Monodelphis domestica	ENSMODG00000015933	1 retrocopy	retro_mdom_426,
Mus musculus	ENSMUSG00000024436	1 retrocopy	retro_mmus_2036,
Nomascus leucogenys	ENSNLEG00000005224	1 retrocopy	retro_nleu_1811,
Oryctolagus cuniculus	ENSOCUG00000002149	2 retrocopies	retro_ocun_1307, retro_ocun_1641,
Pongo abelii	ENSPPYG00000016412	1 retrocopy	retro_pabe_2050,
Pan troglodytes	ENSPTRG00000017932	1 retrocopy	retro_ptro_1648,
Rattus norvegicus	ENSRNOG00000000804	1 retrocopy	retro_rnor_1328,
Ictidomys tridecemlineatus	ENSSTOG00000011853	1 retrocopy	retro_itri_254,
Tarsius syrichta	ENSTSYG00000003333	1 retrocopy	retro_tsyr_1769,